As the human genome comes close to being completely identified, attention is turning to protein characterization, because the proteins are the substances actually involved in physiological processes, individually, posttranslationally modified and/or as part of complexes. State-of-the-art protein identification is based on mass spectrometric characterization of proteolytic peptides, either through peptide mapping data or through sequence tag data, combined with data base searching. In the peptide mapping approach, the masses of proteolytic peptides obtained at high resolution/accuracy are searched against the data base. In the sequence tag approach, the high accuracy (better than 0.1 Da) mass of a single peptide combined with the mass of fragment ions obtained by MS/MS analysis are searched against the data base. Recognizing the importance of protein characterization, we have set up a protein characterization facility within the mass spectrometry group. This facility provides state-of-the-art MS-based characterization of proteins isolated by SDS-PAGE to the Institute, primarily on a collaborative basis. Additionally, the facility will also collaborate on the identification of posttranslational protein modifications and determination of the amino acids modified. The facility is also working with the 2-D gel electrophoresis group (A. Merrick) to form a proteomics working group which has been formed to provide functional proteomics collaborations. In functional proteomics, differential expression of proteins as a consequence of specific physiological states is determined by 2-D gel electrophoresis, and those proteins which have been identified as differentially expressed are then identified by mass spectrometry. The information obtained in these experiments can uncover new and unexpected biological pathways involved in toxicity.